Secondary electron emission control in X-ray photoelectron spectroscopy

Secondary electron emission (SEE) is a major player in surface charging during X-ray photoelectron spectroscopy (XPS); its characteristics and applicability as a current source for electrical measurements are studied. We employ sample biasing and a top retarding grid to control the photoelectron current, and further compare their I–V characteristics with direct spectroscopy of the secondary electrons. Using silica-coated gold substrates, the effect of sample work function on the emitted secondary electrons is shown and fine control over the surface potential gradients, in the range of 10–100 meV, is achieved. XPS-based chemically resolved electrical measurements (CREM) can thus be extended to the positive current regime.     

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.     

Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy S and free energy F from a given MC trajectory developed recently and applied to liquid argon, TIP3P water, and peptides. In this paper HSMC is extended to random coil polymers by applying it to self-avoiding walks on a square lattice--a simple but difficult model due to strong excluded volume interactions. With HSMC the probability of a given chain is obtained as a product of transition probabilities calculated for each bond by MC simulations and a counting formula. This probability is exact in the sense that it is based on all the interactions of the system and the only approximation is due to finite sampling. The method provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation. HSMC is independent of existing techniques and thus constitutes an independent research tool. The HSMC results are compared to those obtained by other methods, and its application to complex lattice chain models is discussed; we emphasize its ability to treat any type of boundary conditions for which a reference state (with known free energy) might be difficult to define for a thermodynamic integration process. Finally, we stress that the capability of HSMC to extract the absolute entropy from a given sample is important for studying relaxation processes, such as protein folding.     

On the zero fluctuation of the “microscopic free energy” and its potential use

The fluctuations of the microscopic free energy calculated with the ensemble probability are shown to be zero. We suggest that this result be used for estimating approximate free energies calculated on the basis of the minimum free energy principle. As an example the estimation is performed with respect to a certain computer simulation of the square Ising lattice. The zero fluctuations also can be used to obtain relations among fluctuations with the accurate ensemble probability distribution.     

Angular broadening in core‐electron spectroscopy

The role of angular broadening in quantitative core‐electron spectroscopy is investigated using an analytic approach. It is shown why, practically, this effect remains relatively small for a broad range of parameters. A correction factor is derived, suggesting that the replacement of inelastic mean free path by an effective attenuation‐length parameter is not necessarily an optimal choice. The derived expression further proposes useful insight on the contribution of leading experimental parameters and, in particular, on the sharp increase of elastic‐scattering corrections above a (depth dependent) critical angle. Copyright © 2015 John Wiley & Sons, Ltd.     

A marked synergistic effect in antitumor activity of salan titanium(IV) complexes bearing two differently substituted aromatic rings

Salan titanium(IV) complexes of differently substituted aromatic rings, where one ring is para-nitrated and another is ortho,para-halogenated, demonstrate exceptionally high anticancer activity, with IC(50) values of <1 μM, exceeding that of cisplatin by ~30-fold. Whereas an additive effect in hydrolytic stability was detected for these highly stable complexes, an unexpected synergistic effect in anticancer activity makes these hybrid complexes substantially more active than both their symmetrical analogues alone and their equimolar mixture.     

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed.     

Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics (MD) techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). With our recent version of HS, called HSMC-EV, each TP is calculated from MC simulations, where the simulated particles are excluded from the volume reconstructed in previous steps. In this paper we remove the excluded volume (EV) restriction, replacing it by a "free volume" (FV) approach. For liquid argon, HSMC-FV leads to an improvement in efficiency over HSMC-EV by a factor of 2-3. Importantly, the FV treatment greatly simplifies the HS implementation for liquids, allowing a much more natural application of the method for MD simulations. Given the success and popularity of MD, the present development of the HSMD method for liquids is an important advancement for HS methodology. Results for the HSMD-FV approach presented here agree well with our HSMC and thermodynamic integration results. The efficiency of HSMD-FV is equivalent to HSMC-EV. The potential use of HSMC(MD)-FV in protein systems with explicit water is discussed.     

The stochastic models method applied to the critical behavior of Ising lattices

The stochastic models (SM) computer simulation method for treating manybody systems in thermodynamic equilibrium is investigated. The SM method, unlike the commonly used Metropolis Monte Carlo method, is not of a relaxation type. Thus an equilibrium configuration is constructed at once by adding particles to an initiallyempty volume with the help of a model stochastic process. The probability of the equilibrium configurations is known and this permits one to estimate the entropy directly. In the present work we greatly improve the accuracy of the SM method for the two and three-dimensional Ising lattices and extend its scope to calculate fluctuations, and hence specific heat and magnetic susceptibility, in addition to average thermodynamic quantities like energy, entropy, and magnetization. The method is found to be advantageous near the critical temperature. Of special interest are the results at the critical temperature itself, where the Metropolis method seems to be impractical. At this temperature, the average thermodynamic quantities agree well with theoretical values, for both the two and three-dimensional lattices. For the two-dimensional lattice the specific heat exhibits the expected logarithmic dependence on lattice size; the dependence of the susceptibility on lattice size is also satisfactory, leading to a ratio of critical exponents/=1.85 ±0.08. For the three-dimensional lattice the dependence of the specific heat, long-range order, and susceptibility on lattice size leads to similarly satisfactory exponents:=0.12 ±0.03,=0.30 ±0.03, and=1.32 ±0.05 (assuming =2/3).